| Variant ID: vg1212722824 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12722824 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 322. )
GGGTCGCTGGGGAGTCCATGCCTCTGGTTATATTTATAGAGGGGGTGATTATGATCCAGGAATGGTGCACTATGGTGAGTTGTGTTGTGCAGGGGGTACT[G/A]
TCACAGCCTCTATTCGGGTACTTTCCAGTATCGCGACGCATGGTAGACATGATGTTGAGGCTGTGTCTTGTGTGTACAGTGGTACACCTCTGGCCAGAGT
ACTCTGGCCAGAGGTGTACCACTGTACACACAAGACACAGCCTCAACATCATGTCTACCATGCGTCGCGATACTGGAAAGTACCCGAATAGAGGCTGTGA[C/T]
AGTACCCCCTGCACAACACAACTCACCATAGTGCACCATTCCTGGATCATAATCACCCCCTCTATAAATATAACCAGAGGCATGGACTCCCCAGCGACCC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.00% | 0.70% | 0.28% | 0.00% | NA |
| All Indica | 2759 | 98.30% | 1.20% | 0.47% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.30% | 0.50% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 97.20% | 2.60% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 98.10% | 0.80% | 1.15% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212722824 | G -> A | LOC_Os12g22530.1 | downstream_gene_variant ; 4370.0bp to feature; MODIFIER | N | Average:57.82; most accessible tissue: Minghui63 young leaf, score: 78.054 | N | N | N | N |
| vg1212722824 | G -> A | LOC_Os12g22540.1 | intron_variant ; MODIFIER | N | Average:57.82; most accessible tissue: Minghui63 young leaf, score: 78.054 | N | N | N | N |